This directory contains the Sep. 2006 assembly of the S. purpuratus genome
(strPur2, Baylor release 3 Spur 2.1), as well as repeat annotations and GenBank sequences.
This assembly was produced by the Baylor College of Medicine Human Genome Sequencing Center.
For more information on the S. purpuratus genome, see the project website:
http://www.hgsc.bcm.tmc.edu/projects/seaurchin/
Files included in this directory:
strPur2.2bit - contains the complete S. purpuratus/strPur2 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
strPur2.agp.gz - Description of how the assembly was generated from
fragments.
strPur2.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
strPur2.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
strPur2.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RepeatMasker version open-3-1-6 Database RepeatMaskerLib.embl
version: 20061006.
strPur2.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
md5sum.txt - checksums of files in this directory
strPur2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then
go to the directory goldenPath/strPur2/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
For conditions of use regarding the S. purpuratus genome sequence data, see
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html .
Name Last modified Size Description
Parent Directory -
strPur2.chrom.sizes 2007-03-12 14:59 2.0M
strPur2.2bit 2007-03-22 14:53 227M
strPur2.agp.gz 2007-05-17 13:32 3.6M
strPur2.fa.out.gz 2007-05-17 13:33 24M
strPur2.trf.bed.gz 2007-05-17 13:33 3.9M
strPur2.fa.gz 2007-05-17 13:37 249M
strPur2.fa.masked.gz 2007-05-17 13:41 213M
md5sum.txt 2014-01-03 15:20 304
mrna.fa.gz 2019-10-16 15:44 28M
mrna.fa.gz.md5 2019-10-16 15:44 45
xenoMrna.fa.gz 2019-10-16 15:55 6.8G
xenoMrna.fa.gz.md5 2019-10-16 15:55 49
est.fa.gz 2019-10-16 16:00 34M
est.fa.gz.md5 2019-10-16 16:00 44
xenoRefMrna.fa.gz 2019-10-16 16:00 330M
xenoRefMrna.fa.gz.md5 2019-10-16 16:00 52
refMrna.fa.gz 2019-10-16 16:00 380K
refMrna.fa.gz.md5 2019-10-16 16:00 48
genes/ 2020-02-05 13:47 -